Media 000398713: Atlas
Open Download
Type Mesh
Modality X-Ray Computed Tomography (CT/microCT)
Media represents biological specimen
Managed by

Media Display

GENERAL DETAILS Field Definitions

Media ID
000398713
Media type
Mesh
Object element or part
atlas
Object represented
Object taxonomy
Marmorerpeton kermacki
Side
--
Orientation
--
Short description
Surface model
Full description
Segmented using Amira 6.7.0. Thresholding was used to determine the general boundary of the bone (by Roger Benson) and matrix was removed with manual segmentation (by Marc Jones). The final segmentation was inspected and manually edited using all three slice planes. Surface models were generated using Algorithim mode repeatable and Unconstrained smoothing set at 2. The thumbnail screenshot was taken in orthographic view.
Creator
Benson, Roger; Jones, Marc
Date created
November 22, 2021
Date uploaded
November 29, 2021

FILE OBJECT DETAILS Field Definitions

File name
Marmorerpeton_kermacki_NHMUK_R11361_atlas_uncon_2_.ply
File format(s)
PLY
File size
633 MB
Points
8101672
Polygons
16202372
Map type
--
UV coordinates
False
Vertex color
False
Bounding box dimensions
5.556, 5.566, 4.562
Centroid coordinates
3.110, 3.206, 2.424
Units of point coordinates
Mm

IMAGE ACQUISITION AND PROCESSING AT A GLANCE Field Definitions

Number of parent media
1
Number of processing events
2 (0 steps)
Modality
X-Ray Computed Tomography (CT/microCT)
Device
Nikon HMX ST 225, UCL Division of Biosciences (University College London)

OWNERSHIP AND PERMISSIONS Field Definitions

Data managed by
Data uploaded by
Publication status
Open Download
IP holder
The Trustees of the Natural History Museum, London
Morphosource use agreement type
Standard
Permits commercial use
Commercial Use Not Permitted
Permits 3D use
3D Printing Limited
Required archival of published derivatives
On MorphoSource
Funding attribution
Leverhulme Trust research project grant RPG-2018-381
Publisher
Benson, Roger; Jones, Marc
Cite as
Roger Benson provided access to these data, originally appearing in Jones et al. (2022 "Middle Jurassic fossils document an early stage in salamander evolution"), the collection of which was funded by Leverhulme Trust research project grant RPG-2018-381. The files were downloaded from www.MorphoSource.org, Duke University. © The Trustees of the Natural History Museum, London
Media preview mode
Interactive/Embeddable
Additional usage agreement
None

IDENTIFIERS AND EXTERNAL LINKS Field Definitions

MorphoSource ARK
MorphoSource DOI
Not assigned
External identifier
--
External media URL
--

IMAGE ACQUISITION AND PROCESSING IN DETAIL

STEP 1: IMAGE ACQUISITION

Physical object NHMUK:PAL:PV R 11361 was imaged to create undeposited raw media.

IMAGING DETAILS Field Definitions

Modality
X-Ray Computed Tomography (CT/microCT)
Device
Nikon HMX ST 225
Device facility
UCL Division of Biosciences (University College London)
Creator
Benson, Roger
Event date
--
Software
--
Description
--
Description attachment
None
Reference attachment
None
Exposure time
0.254
Flux normalization
--
Pixel spacing calibration
--
Shading correction
--
Frame averaging
1
Projections
501
Voltage
55
Power
--
Amperage
91
Surrounding material
--
X-ray tube type
--
Target type
--
Detector type
--
Detector pixels X
--
Detector pixels size X
--
Detector pixels Y
--
Detector pixels size Y
--
Detector configuration
--
Source object distance
--
Source detector distance
--
Target material
--
Rotation number
--
Phase contrast
--
Optical magnification
--
Acquisition type
--

STEP 2: IMAGE PROCESSING

Raw media (undeposited) was processed to create derived Media 000398710: Atlas [CTImageSeries] [CT].

Processing Details Field Definitions

Creator
Benson, Roger
Event date
--
Software
CT 3D Pro
Description
reconstruct tomograms
Description attachment
None

Media produced by this event on MorphoSource

STEP 3: IMAGE PROCESSING

Derived Media 000398710: Atlas [CTImageSeries] [CT] was processed to create derived Media 000398713: Atlas [Mesh] [CT] (this media).

Processing Details Field Definitions

Creator
Benson, Roger
Event date
--
Software
Avizo
Description
segmentation
Description attachment
None

Media produced by this event on MorphoSource

Media 000398713: Atlas [Mesh] [CT] (this media)